02/13/2016

	. The consensus tutorials have been updated to refect results of
	  the WGCNA package version 1.49 current as of February 2016.

06/15/2014

	. Added plain text R scripts isolated from the tutorials for easier
	  copying and pasting.

11/25/2014

	. Adapted tutorials for the upcoming WGCNA version 1.42. The main
	  change is replacing calls to flashClust with hclust, since WGCNA
	  will from now on use the hclust function implemented in the package
	  fastcluster.

06/04/2014

	. Fixed wrong statements in Tutorial I, section 5, concerning which
	  modules are part of the same meta-module (thanks to Susan Service
	  for pointing this out

02/14/2014

	. Added setLabels to the save call at the end of Tutorial II, Section 1.
	  (Thanks to Kazuhiro Fujita for pointing this out.)

	. Added warnings about incompatibility of RStudio with parallel
	  computation in the relevant tutorial sections.


07/19/2013

	. Corrected arguments to blockwiseModules to reproduce results in 
	  the tutorial.

02/21/2013:

	. A discrepancy between merging heights in Sections 2.a and 2.b of
	  Tutorial I has been corrected (thanks to Junfeng Jiang for pointing it
	  out)

	. Argument minKMEtoStay has been removed from calls to
	  blockwiseConsensusModules since the function does not accept the
	  argument anymore (also thanks to Junfeng Jiang for pointing it out).

12/24/2012:

	. A bug in Tutorial II, section 2 fixed (previously undefined variable
	  'nSets' is now defined).

11/20/2012:

	. A bug in Tutorial I, section 6a fixed (`order' replaced by `rank').

11/13/2012:

	. Adapted tutorials to the new multi-threading/parallel computation
	  functions, in particular changed some calls to allowWGCNAThreads to
	  enableWGCNAThreads.

12/07/2011:

	. Fixed function name plotMat from plot.Mat
	. Fixed component name cor.Weighted from Cor.Weighted

06/06/2011:

	. Added link to Jeremy Miller's more advanced tutorial
	. Added a subsection on export of network analysis results 
	  to Tutorial II, Section 4.

01/07/2010: 

	. Tutorial I, Section 4b rewritten to illustrate GO enrichment
	  analysis directly within the WGCNA package using the function
	  GOenrichmentAnalysis

11/17/2009:

	. small changes in Tutorial I, section 5, plotEigengeneNetworks to
	  make the plot look better.
	. bugfix in Tutorial II, section 5: definition of missing variables
	  added in the beginning

10/19/2009:

	. adapted Tutorial III (Analysis of simulated data) to WGCNA version 0.81 
	  that contains the necessary functions from the now defunct package sma, 
	  and removed loading of the sma package.

09/09/2009:

	. typo fixed in Tutorial II (Consensus analysis), section 1c (thanks to Michael Zhou 
	  for pointing it out)

09/04/2009:

	. from now on the file GeneAnnotation.csv is not gzip-ed as it seems to lead to occasional
	  problems. The tutorials have been adapted to read the un-gzip-ed csv file.

09/03/2009:

	. adapted code to new version of GOSim by changing 'analyzeCluster' to 'GOenrichment'

06/02/2009:

	. added setting the working directory at the beginning of the analysis

05/08/2009:

	. added cautionary notes about arguments to blockwise[Consensus]Modules

03/18/2009:

	. reworked blockwise module detection to reflect the improvements in
	  pre-clustering algorithms and illustrate the use of matchLabels in
	  comparing different clusterings
	. added comparison of single-block and block-wise methods for female
	  mouse tutorial
	. fixed typos, errors, and inconsistencies in consensus tutorials

03/03/2009:

	. fixed a bug in the consensus tutorial part 2.b: unmergedColors are now properly defined 
	  (thanks to Dave Weston for pointing it out)

02/20/2009:

	. Added a short section of code to both mouse tutorials to illustrate removal of bad genes and
	  samples identified by the functions goodSamplesGenes, goodSamplesGenesMS

02/05/2009:

	. Adapted tutorials to WGCNA version 0.71 and dynamicTreeCut 1.20. Results are unchanged. 
	  Note that current tutorials are not compatible with earlier versions of WGCNA and
	  dynamicTreeCut.

12/22/2008:

	. Added simulated data tutorial
	. Mouse tutorials: changed module merging cut to 0.25, resulting in
	  slightly fewer and larger modules